GO analysis of Soybean

Question

[hrhki2015]

I'm working on the expression analysis of soybean. The expression was analyzed by RNA-seq with RStudio, but GO analysis with the software have the error.

The software was RStudio Version 1.1.442.

library(org.XX.xxx.db) 

library(goProfiles)

x <- read.csv("induction.txt", header=TRUE, sep=",")

head(x, n=3)
           name    logFC   logCPM       PValue          FDR
1 GLYMA01G26750 4.002202 7.114714 9.781341e-29 1.613378e-26
2 GLYMA14G05850 3.427588 6.409440 5.438084e-26 5.381890e-24
3 GLYMA02G17940 4.585453 2.839647 5.506072e-25 5.108602e-23

Above is all right. So next has a problem...

induction <- basicProfile(genelist=x$name, onto='ANY', level=2, orgPackage="org.XX.xxx.db")

if I submit the "MeSH.Gma.eg.db" instead of "org.XX.xxx.db", the software return

eval(parse(text = envirName)) with error.

Could you explain and write the R code for the analysis? Can't I use "MeSH.Gma.eg.db" for the GO analysis? If you know the GO analysis with a different way, please let me know.

I'm not still used to R..

Haru

[Buffo]

I think WebGestalt would be useful for you, it translates gene sets to biological insights.